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(-) Description

Title :  CRYSTAL STRUCTURE OF CREATINE-ADP ARGININE KINASE TERNARY COMPLEX
 
Authors :  A. Azzi, S. A. Clark, R. W. Ellington, M. S. Chapman
Date :  25 Nov 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Arginine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Azzi, S. A. Clark, W. R. Ellington, M. S. Chapman
The Role Of Phosphagen Specificity Loops In Arginine Kinase.
Protein Sci. V. 13 575 2004
PubMed-ID: 14978299  |  Reference-DOI: 10.1110/PS.03428304
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE KINASE
    Chains: A
    EC Number: 2.7.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Common: ATLANTIC HORSESHOE CRAB
    Organism Scientific: LIMULUS POLYPHEMUS
    Organism Taxid: 6850
    Synonym: AK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2IOM1Ligand/Ion(DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:429 , HOH A:570 , HOH A:573 , HOH A:576 , ADP A:900BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWARESER A:122 , ARG A:124 , ARG A:126 , HIS A:185 , TRP A:221 , ARG A:229 , ARG A:280 , SER A:282 , VAL A:283 , HIS A:284 , ARG A:309 , THR A:311 , ARG A:312 , GLY A:313 , GLU A:314 , ASP A:324 , HOH A:364 , HOH A:387 , HOH A:396 , HOH A:429 , HOH A:471 , HOH A:570 , HOH A:573 , HOH A:576 , HOH A:584 , MG A:901BINDING SITE FOR RESIDUE ADP A 900
3AC3SOFTWAREVAL A:65 , GLU A:225 , CYS A:271 , THR A:273 , ASN A:274 , GLU A:314 , HOH A:399 , HOH A:439 , HOH A:450 , HOH A:501 , HOH A:609 , HOH A:661BINDING SITE FOR RESIDUE IOM A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RL9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:204 -Pro A:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RL9)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHAGEN_KINASE_NPS51509 Phosphagen kinase N-terminal domain profile.KARG_LIMPO9-91  1A:9-91
2PHOSPHAGEN_KINASE_CPS51510 Phosphagen kinase C-terminal domain profile.KARG_LIMPO119-356  1A:119-356
3PHOSPHAGEN_KINASEPS00112 Phosphagen kinase active site signature.KARG_LIMPO271-277  1A:271-277

(-) Exons   (0, 0)

(no "Exon" information available for 1RL9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:356
 aligned with KARG_LIMPO | P51541 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:356
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      
           KARG_LIMPO     2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPGGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
               SCOP domains d1rl9a1 A:2-95 Arginine kinase, N-domain                                                      d1rl9a2 A:96-357 Arginine kinase, C-terminal domain                                                                                                                                                                                                                    SCOP domains
               CATH domains 1rl9A01 A:2-95 Transferase Creatine Kinase, Chain A, domain 1                                 --1rl9A02 A:98-357 Creatine Kinase; Chain                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------ATP-gua_PtransN-1rl9A02 A:18-93                                             --------------------ATP-gua_Ptrans-1rl9A01 A:114-356                                                                                                                                                                                                                   - Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh.......hhhhhhh..........eeee.....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeee......hhhhhhhhhhh..eeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PHOSPHAGEN_KINASE_N  PDB: A:9-91 UniProt: 9-91                                     ---------------------------PHOSPHAGEN_KINASE_C  PDB: A:119-356 UniProt: 119-356                                                                                                                                                                                          - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rl9 A   2 VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GCS (23)
(-)
Clan: no clan defined [family: ATP-gua_PtransN] (14)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KARG_LIMPO | P51541)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004054    arginine kinase activity    Catalysis of the reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + 2 H(+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1rl9
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  KARG_LIMPO | P51541
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  2.7.3.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KARG_LIMPO | P51541: 1bg0 1m15 1p50 1p52 1sd0 3m10 4gvy 4gvz 4gw0 4gw2 5j99 5j9a

(-) Related Entries Specified in the PDB File

1bgo THE SAME PROTEINE COMPLEXED WITH ADP, NITRATE AND ARGININE